How can I prevent blender from exporting fbx with-90 rotation on the x axis to unity?
If you don't want to use scripts, here is another workflow:


Select every object that will be exported, but no child-objects of these, even if they will be exported too
Rotate them by -90 degrees in the x-axis
Apply the rotation of every object that will be exported (the child-objects included)
Select the objects from (1) again and rotate them back by 90 degrees in the x-axis


Make sure that the pivot point for each rotation is the same (e.g. individual origins), so that the objects will end up in their original position and make sure that you apply the rotation of every object in one action, or else the rotation of the child-objects changes again.